Hello again! My problem with implicit solvent is still unsolved. In gromacs manual and in gmx-users mail list was also mentioned that for implicit salvation all cut-offs should be switched to zeros. In that case PBC don't work. I've tried to perform simulation with implicit solvent and usual cut-offs of 1,4 nm, but protein tertiary structure eventually after 1 ns started to collapse: different alpha-chains twisted around each other moved from each other. It seems like protein gained denaturation after. But it was ok with explicit solvent along 150 ns simulation.
So that is the question: If it is possible to use PBC and periodic molecules with implicit solvent, what value for cut-offs should I take? My system is a big protein of 340 kDa and a graphite sheet. Thanks in advance for answers. С уважением, Толстова Анна 2015-10-29 14:48 GMT+03:00 Vitaly V. Chaban <vvcha...@gmail.com>: > Yes. It is formally possible. > > I do not think that implicit solvation precludes PBC usage. > > > > > > > > > On Thu, Oct 29, 2015 at 9:40 AM, Анна Павловна Толстова < > tolst...@physics.msu.ru> wrote: > > > Hello, gmx_users. > > > > Is that possible to simulate a protein adsorption on graphite sheet with > > implicit solvent? It works good in vacuo and with explicit solvent with > > periodic-molecules = yes. But implicit solvent requires no PBC so that > > periodic molecules should be switched off too. Is there any idea how to > > perform this simulation? > > > > Best wishes, > > Tolstova Ann > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
